Relax libhdf version and update CI to test system libhdf5

[musm]

Summary of changes:

• Relax libhdf5 to v1.10.4 (this is the version shipped with ubuntu-lts)
• Merge all CI into one file (easier to maintain and update)
• Test libhdf5 + mpio integration on CI

[musm]

@jipolanco I'm running into

Attempting to use an MPI routine before initializing MPICH
HDF5: infinite loop closing library
      L,T_top,P,P,Z,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD

when I run the test with with MPI. This is on my system with:

sudo apt install libhdf5-mpich-dev
export JULIA_HDF5_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/hdf5/mpich/

Any chance you would know why we are running into this?

In particular it looks like this method is triggering the error

    HDF5.h5p_set_fapl_mpio(fileprop, comm, info)

in the mpio.jl test suite.

[musm]

change to ubuntu-latest when gh-actions get's updated (required for libhdf5 v1.10.4)

[jipolanco]

@jipolanco I'm running into

Attempting to use an MPI routine before initializing MPICH
HDF5: infinite loop closing library
      L,T_top,P,P,Z,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD

when I run the test with with MPI. This is on my system with:

sudo apt install libhdf5-mpich-dev
export JULIA_HDF5_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/hdf5/mpich/

Any chance you would know why we are running into this?

In particular it looks like this method is triggering the error

    HDF5.h5p_set_fapl_mpio(fileprop, comm, info)

in the mpio.jl test suite.

@musm I'm not sure, but it may be because you're not using your system's MPICH. For this, you should set the environment variable JULIA_MPI_BINARY=system and then rebuild MPI.jl and HDF5.jl.

You may also be interested in this github CI setup using MPI and HDF5 on Ubuntu.

[musm]

That was very helpful, many thanks @jipolanco

[jipolanco]

No problem. Thanks for the extra tests and for relaxing the libhdf5 requirement!